Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
- ======================================================================-====*/
+ ===========================================================================**/
#ifndef CLITKEXTRACTBONESSGENERICFILTER_TXX
#define CLITKEXTRACTBONESSGENERICFILTER_TXX
template<unsigned int Dim>
void clitk::ExtractBonesGenericFilter<ArgsInfoType>::InitializeImageType()
{
- ADD_IMAGE_TYPE(Dim, short);
+ //ADD_IMAGE_TYPE(Dim, short);
// ADD_IMAGE_TYPE(Dim, int);
- // ADD_IMAGE_TYPE(Dim, float);
+ ADD_IMAGE_TYPE(Dim, float);
}
//--------------------------------------------------------------------
void clitk::ExtractBonesGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a)
{
mArgsInfo=a;
- SetIOVerbose(mArgsInfo.verbose_flag);
+ this->SetIOVerbose(mArgsInfo.verbose_flag);
if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
- if (mArgsInfo.input_given) AddInputFilename(mArgsInfo.input_arg);
- if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg);
+ if (mArgsInfo.input_given) this->AddInputFilename(mArgsInfo.input_arg);
+ if (mArgsInfo.output_given) this->AddOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void clitk::ExtractBonesGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+ f->SetVerboseOptionFlag(mArgsInfo.verboseOption_flag);
+ f->SetVerboseStepFlag(mArgsInfo.verboseStep_flag);
+ f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
+ f->SetVerboseWarningFlag(!mArgsInfo.verboseWarningOff_flag);
+ f->SetVerboseMemoryFlag(mArgsInfo.verboseMemory_flag);
+
+ if (mArgsInfo.afdb_given)
+ f->SetAFDBFilename(mArgsInfo.afdb_arg);
+
+ f->SetOutputBonesFilename(mArgsInfo.output_arg);
+
+ f->SetInitialSmoothing(mArgsInfo.smooth_flag);
+ f->SetSmoothingConductanceParameter(mArgsInfo.cond_arg);
+ f->SetSmoothingNumberOfIterations(mArgsInfo.iter_arg);
+ f->SetSmoothingTimeStep(mArgsInfo.time_arg);
+ f->SetSmoothingUseImageSpacing(mArgsInfo.spacing_flag);
+
+ f->SetMinimalComponentSize(mArgsInfo.minSize_arg);
+ f->SetUpperThreshold1(mArgsInfo.upper1_arg);
+ f->SetLowerThreshold1(mArgsInfo.lower1_arg);
+ f->SetFullConnectivity(mArgsInfo.full_flag);
+
+ f->SetUpperThreshold2(mArgsInfo.upper2_arg);
+ f->SetLowerThreshold2(mArgsInfo.lower2_arg);
+
+ typename FilterType::InputImageSizeType s;
+ if (mArgsInfo.radius2_given) {
+ ConvertOptionMacro(mArgsInfo.radius2, s, 3, false);
+ f->SetRadius2(s);
+ }
+
+ f->SetSampleRate2(mArgsInfo.sampleRate2_arg);
+ f->SetAutoCrop(!mArgsInfo.noAutoCrop_flag);
+ f->SetFillHoles(!mArgsInfo.doNotFillHoles_flag);
}
//--------------------------------------------------------------------
void clitk::ExtractBonesGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
{
// Mask & output image type
- typedef itk::Image<uchar, ImageType::ImageDimension> OutputImageType;
+ typedef itk::Image<uchar, ImageType::ImageDimension> MaskImageType;
// Reading input
typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
// Create filter
- typedef clitk::ExtractBonesFilter<ImageType, OutputImageType> FilterType;
+ typedef clitk::ExtractBonesFilter<ImageType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
// Set global Options
- filter->SetArgsInfo(mArgsInfo);
filter->SetInput(input);
+ SetOptionsFromArgsInfoToFilter<FilterType>(filter);
// Go !
filter->Update();
- // Check if error
- if (filter->HasError()) {
- SetLastError(filter->GetLastError());
- // No output
- return;
- }
-
// Write/Save results
- typename OutputImageType::Pointer output = filter->GetOutput();
- this->template SetNextOutput<OutputImageType>(output);
+ typename MaskImageType::Pointer output = filter->GetOutput();
+ this->template SetNextOutput<MaskImageType>(output);
}
//--------------------------------------------------------------------